Taxonomic profiling of bacterial and archaeal communities from saliva, stool, and CapScan-sampled gut metagenomes

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Subject: TS

1.1 Overview of microbial community composition

Figure 1 is an interactive figure showing the microbial community composition in each collected sample. Here, each color and shade corresponds to a different genus. For reference, domestic dogs (Canis familiaris) and gray wolves (Canis lupus) are different species that belong to the same genus (Canis).

You can interact with this figure by:

• Hovering the cursor over a color in the stacked bar to see the taxonomic identity, sample type, and relative abundance corresponding to that color and bar
• Clicking and dragging the cursor over a portion of the figure to zoom
• Single-clicking a genus’s name in the legend to remove that genus from the figure
• Double-clicking a genus’s name in the legend to only show that genus

Figure 1: Microbial community composition of collected saliva, stool, and CapScan samples. CapScan samples are ordered from proximal to distal intestine (i.e., increasing distance from mouth). Taxonomic composition is reported at the genus rank. Genera present at <1% relative abundance across all samples are reported as “Other genera”. Note: Blue = Firmicutes; Yellow = Actinomycetes; Green = Bacteroidetes; Red = Proteobacteria; Purple = all other phyla. Shades of the same color (except purple) correspond to different genera from the same phylum.

1.2 High-resolution snapshot of community composition

Figure 2 is an interactive figure showing the microbial community composition at higher taxononomic resolution. Here, each row corresponds to a unique microbe.

You can interact with this figure by:

• Hovering the cursor over a cell to see that microbe’s genus and species (and strain when available), relative abundance, and full taxonomic classification
• Clicking and dragging the cursor over a portion of the figure to zoom

Figure 2: Heat map showing relative abundance of microbes in each sample (N = 266 total identified). Each row corresponds to a unique microbe and each column corresponds to an individual sample. Note the relative abundance colorscale is in log units.

1.3 Notable microbes detected

• Raoultella ornithinolytica:
  • Previously identified strains produce histamine from histidine (an amino acid) (Kanki et al., 2002), which can trigger an inflammatory response by the immune system
  • Found in high relative abundance in proximal CapScan samples (~15-25%)
    
    
• Klebsiella pneumoniae:
  • A known cause of pneumonia by inducing inflammation upon colonization of the lungs; growing interest in the connection between Klebsiella pneumoniae and inflammatory bowel diseases (reviewed in Kaur et al., 2018)
  • Detected in CapScan samples (~2% relative abundance) but not stool

1.4 References

Kanki, M., Yoda, T., Tsukamoto, T., and Shibata, T. (2002) Klebsiella pneumoniae produces no histamine: Raoultella planticola and Raoultella omithinolytica strains are histamine producers. Appl Environ Microbiol 68: 3462–3466.

Kaur, C.P., Vadivelu, J., and Chandramathi, S. (2018) Impact of Klebsiella pneumoniae in lower gastrointestinal tract diseases. J Dig Dis 19: 262–271.